The Nongame Program is responsible for managing species legally designated as Nongame, which includes Species of Greatest Conservation Need with a designated Native Species Status (NSS) and Neotropical Migratory Birds (NTMB). Using the Native Species Status matrix that first appeared in the Nongame Bird and Mammal Plan (Oakleaf et al. 1996) and has since been updated and included in the Department's Comprehensive Wildlife Conservation Strategy (2005), the Department has designated Species of Greatest Conservation Need with a Native Species Status of 1, 2, 3, or 4.

The Nongame Program is also responsible for cooperative management with the U.S. Fish and Wildlife Service of the following federally listed Threatened or Endangered species: Brown Pelican, Wood Stork, Whooping Crane, Piping Plover, Least Tern, blackfooted ferret, and Canada lynx.